NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P56408 UniProt NPD GO	FER_CHLFU	Ferredoxin	0.00	-	nuc	0	Plastid; chloroplast			1AWD	94
P00222 UniProt NPD GO	FER_COLES	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P83520 UniProt NPD GO	FER_DATAR	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P68167 UniProt NPD GO	FER_DATFA	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P68163 UniProt NPD GO	FER_DATIN	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P68164 UniProt NPD GO	FER_DATME	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P68166 UniProt NPD GO	FER_DATQU	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P68165 UniProt NPD GO	FER_DATST	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P83523 UniProt NPD GO	FER_LYCCN	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P09735 UniProt NPD GO	FER_MARPO	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				95
P00220 UniProt NPD GO	FER_MEDSA	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P83524 UniProt NPD GO	FER_PHYAF	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P00226 UniProt NPD GO	FER_SAMNI	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P83525 UniProt NPD GO	FER_SCOJA	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P83585 UniProt NPD GO	FER_SOLAB	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P83584 UniProt NPD GO	FER_SOLLS	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P83583 UniProt NPD GO	FER_SOLLY	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P83582 UniProt NPD GO	FER_SOLNI	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
O98450 UniProt NPD GO	FER_THAWE	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				98
P83526 UniProt NPD GO	FER_TOBAC	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS]			97
P18820 UniProt NPD GO	FER_PORAE	Ferredoxin (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				33
P18821 UniProt NPD GO	FER_PORCR	Ferredoxin (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				32
P34806 UniProt NPD GO	FER_PSALA	Ferredoxin precursor	0.00	-	mit	0	Hydrogenosome				107
P14938 UniProt NPD GO	FER3_RAPSA	Ferredoxin, leaf L-A	0.00	-	nuc	0	Plastid; chloroplast				96
P14936 UniProt NPD GO	FER1_RAPSA	Ferredoxin, root R-B1	0.00	-	cyt	0	Plastid; chloroplast				98
P14937 UniProt NPD GO	FER2_RAPSA	Ferredoxin, root R-B2	0.00	-	nuc	0	Plastid; chloroplast				98
Q43090 UniProt NPD GO	NIR_PINSY	Ferredoxin--nitrite reductase, chloroplast (EC 1.7.7.1) (NiR) (PSNiR) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				105
P00235 UniProt NPD GO	FER1_EQUAR	Ferredoxin-1 (Ferredoxin I)	0.00	-	cyt	0	Plastid; chloroplast			1FRR	95
P00234 UniProt NPD GO	FER1_EQUTE	Ferredoxin-1 (Ferredoxin I)	0.00	-	cyt	0	Plastid; chloroplast				95
P00229 UniProt NPD GO	FER1_PHYAM	Ferredoxin-1 (Ferredoxin I)	0.00	-	cyt	0	Plastid; chloroplast				96
P00230 UniProt NPD GO	FER1_PHYES	Ferredoxin-1 (Ferredoxin I)	0.00	-	cyt	0	Plastid; chloroplast				96
P84873 UniProt NPD GO	FER1_HYONI	Ferredoxin-1 (Major ferredoxin)	0.00	-	cyt	0	Plastid; chloroplast				97
P09911 UniProt NPD GO	FER1_PEA	Ferredoxin-1, chloroplast precursor (Ferredoxin I)	0.00	-	mit	0	Plastid; chloroplast				149
P00237 UniProt NPD GO	FER2_EQUAR	Ferredoxin-2 (Ferredoxin II)	0.00	-	cyt	0	Plastid; chloroplast			1WRI	93
P00236 UniProt NPD GO	FER2_EQUTE	Ferredoxin-2 (Ferredoxin II)	0.00	-	cyt	0	Plastid; chloroplast				93
P00231 UniProt NPD GO	FER2_PHYAM	Ferredoxin-2 (Ferredoxin II)	0.00	-	cyt	0	Plastid; chloroplast				98
P00232 UniProt NPD GO	FER2_PHYES	Ferredoxin-2 (Ferredoxin II)	0.00	-	cyt	0	Plastid; chloroplast				98
P84874 UniProt NPD GO	FER2_HYONI	Ferredoxin-2 (Minor ferredoxin)	0.00	-	cyt	0	Plastid; chloroplast				97
P81373 UniProt NPD GO	FERB_ALOMA	Ferredoxin-B (Fd B)	0.00	-	cyt	0	Plastid; chloroplast				98
P80680 UniProt NPD GO	FTRV_MAIZE	Ferredoxin-thioredoxin reductase, variable chain (FTR-V) (Ferredoxin-thioredoxin reductase subunit A ...	0.00	-	cyt	0	Plastid; chloroplast				97
P80145 UniProt NPD GO	FRIH_ANAPL	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit) (Prosome-like particle) (PLP) (RNP particle) ...	0.00	-	cyt	0					32
P18686 UniProt NPD GO	FRIL_SHEEP	Ferritin light chain (Ferritin L subunit) (Fragment)	0.00	-	cyt	0					43
P41822 UniProt NPD GO	FRI_AEDAE	Ferritin subunit precursor (EC 1.16.3.1) (Ferritin heavy chain-like protein) (AeFer(H))	0.00	-	mit	0	Secreted protein				209
Q9HGR3 UniProt NPD GO	FAEB_NEUCR	Feruloyl esterase B precursor (EC 3.1.1.73) (Ferulic acid esterase B) (FAEB)	0.00	-	vac	0	Secreted protein (By similarity)	extracellular region [ISS]			292
P82150 UniProt NPD GO	FERT_TOBAC	Feruloyl-CoA thioesterase (EC 3.1.2.-) (Fragment)	0.00	-		0					14
P22775 UniProt NPD GO	FIBR_PANIN	Fibrinogen (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				30
P14442 UniProt NPD GO	FIBA_BUBBU	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P14444 UniProt NPD GO	FIBA_CAMDR	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				18
P68215 UniProt NPD GO	FIBA_CAPHI	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P68216 UniProt NPD GO	FIBA_CEREL	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19

You are viewing entries 94551 to 94600 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.